Contacts of the strand formed by residues 335 - 342 (chain B) in PDB entry 2F61
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 5.5 1.6 - - + -
228B TRP* 3.8 28.7 - - + -
279B LEU* 3.9 9.4 - - + -
306B HIS* 3.3 40.1 + - + +
307B GLY* 3.7 9.4 - - - -
308B ILE* 2.8 32.3 + - - +
332B PRO 5.9 0.2 - - - -
333B ASN 3.8 3.4 + - - -
334B THR* 1.3 73.8 - - - +
336B LEU* 1.3 55.8 + - - +
337B PHE* 3.9 22.0 - - + -
376B VAL* 4.2 31.0 - - + -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.4 2.7 - - + -
308B ILE* 3.5 24.0 - - + +
310B VAL* 4.8 2.2 - - + -
324B LEU* 3.5 47.1 - - + +
327B THR* 3.9 22.2 - - + -
328B HIS* 4.3 11.4 - - + +
334B THR 4.6 4.5 - - - +
335B MET* 1.3 75.1 - - - +
337B PHE* 1.3 57.9 + - - +
373B TYR 3.8 17.9 - - - +
374B HIS* 4.2 14.8 + - + +
375B VAL* 4.0 18.4 - - + -
376B VAL* 2.9 32.6 + - - +
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS* 4.5 3.6 - - + -
118B ILE* 3.7 26.2 - - + -
175B LEU* 3.8 21.5 - - + -
228B TRP* 3.9 23.8 - + - -
279B LEU* 4.3 13.7 - - + -
308B ILE 2.9 11.8 + - - +
309B ALA* 3.0 7.4 - - + -
310B VAL* 2.8 33.8 + - - +
335B MET* 3.9 15.7 - - + -
336B LEU* 1.3 76.2 - - - +
338B ALA* 1.3 60.2 + - - +
339B SER* 3.4 8.2 + - - -
375B VAL* 4.0 3.1 - - - +
376B VAL* 4.1 8.3 - - + -
377B GLY* 3.4 33.7 - - - -
379B THR* 3.1 27.1 - - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.4 9.4 - - + -
312B TRP* 4.1 19.3 - - + -
337B PHE* 1.3 74.2 - - - +
339B SER* 1.3 58.1 + - - +
340B GLU 3.6 3.4 - - - +
370B ASN* 4.1 7.6 - - - +
375B VAL* 3.6 3.0 - - + +
377B GLY 3.0 19.4 + - - +
378B TRP* 3.4 29.1 - - + -
379B THR* 2.8 28.3 + - - +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 3.4 22.0 + - - -
175B LEU* 4.0 14.8 - - - -
282B ASP* 2.7 28.3 + - - -
309B ALA* 3.4 12.7 - - - +
310B VAL 3.0 5.1 + - - -
311B HIS* 3.3 6.8 - - - -
337B PHE* 3.4 18.5 + - - -
338B ALA* 1.3 73.2 - - - +
340B GLU* 1.3 64.0 + - - +
379B THR* 3.5 19.2 - - - +
380B ASP 4.8 1.0 - - - +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 2.8 24.3 + - - +
179B TRP* 3.8 10.0 - - - -
234B ASN* 3.7 10.9 + - - +
235B GLU* 3.9 7.5 - - - +
310B VAL 3.8 2.3 + - - +
311B HIS* 3.3 30.0 + - + +
312B TRP* 2.6 34.4 + - - +
313B TYR* 4.0 13.0 + - - -
338B ALA* 3.6 1.5 - - - -
339B SER* 1.3 82.5 + - - +
341B ALA* 1.3 59.8 + - - +
342B CYS* 5.3 2.9 - - - -
379B THR 3.1 9.8 + - - -
380B ASP 4.9 0.7 - - - -
381B TRP* 3.9 38.2 + - + -
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 3.0 20.4 - - + +
314B LEU* 4.7 3.6 - - + -
338B ALA* 6.3 0.4 - - + -
340B GLU* 1.3 80.2 - - - +
342B CYS* 1.3 66.8 + - - +
363B TYR* 4.3 0.9 - - - -
378B TRP* 3.4 42.8 - - + +
379B THR 3.4 6.2 + - - +
380B ASP* 3.2 21.3 - - - +
381B TRP* 3.3 8.9 + - - +
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Residues in contact with CYS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP 3.3 4.5 + - - -
313B TYR* 4.0 32.5 - - - -
314B LEU* 3.2 26.1 + - - +
315B ASP* 4.5 1.1 + - - +
340B GLU* 5.3 3.6 - - - -
341B ALA* 1.3 79.2 - - - +
343B VAL* 1.3 67.4 + - - +
345B SER* 4.8 3.5 + - - -
363B TYR* 4.0 9.9 - - - +
381B TRP* 4.3 25.6 - - + -
398B VAL* 4.5 21.8 - - + -
399B ASP 4.9 4.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il